Index

_

_ababnehEtAlStatsAndProbs() (Alignment method) _allocCStuff() (Tree method) _commonCStuff() (Tree method) _compareSplitsBetweenTwoTreePartitions() (in module p4.func) _doNodeInfo() (Tree method) _doTimeCheck() (Mcmc method) (STMcmc method) _ladderize() (Node method) _makeChainsAndProposals() (Mcmc method) (STMcmc method) _makeProposals() (Mcmc method) (STMcmc method)

_makeRCSplitKeys() (Tree method) _qj_extractFullyBifurcatingTree() (QuartetJoining method) _refreshProposalProbs() (Mcmc method) _refreshProposalProbsAndTunings() (STMcmc method) _setLogger() (Mcmc method) (STMcmc method) _setOutputTreeFile() (Mcmc method) (STMcmc method) _stdErrorOfTheDifferenceBetweenTwoMeans() (in module p4.func) _sumOfColumns() (in module p4.func) _sumOfRows() (in module p4.func) _sumOfSquares() (in module p4.func)

A

addLeaf() (Tree method) addLeafToBigT() (QuartetJoining method) addNodeBetweenNodes() (Tree method) addSibLeaf() (Tree method) addSubTree() (Tree method) addUnusedTaxaIfTheyHaveThreeKBrs() (QuartetJoining method) addXSubTreeToBigT() (QuartetJoining method) Alignment (class in p4.alignment) alignment() (SequenceList method)

alignments (Var attribute) allBiRootedTrees() (Tree method) allChooseFour() (QuartetJoining method) ancestralStateDraw() (Tree method) andMasks() (Alignment method) areConsistentWithTree() (Constraints method) areConsistentWithTreeRoot() (Constraints method) argvAfterDoubleDash (Var attribute) arithmeticMeanOfLogs() (Numbers method) attachRooter() (Tree method)

B

bigXSquaredSubM() (Tree method) binSize (Numbers property) bionj() (DistanceMatrix method) bluntEndLigate() (Alignment method) bootstrap() (Alignment method) (Data method)

breakTie() (QuartetJoining method) BRLEN_MAX (Var property) BRLEN_MIN (Var property) btv() (Tree method) buildDecoratedTree() (SuperTreeSupport method)

C

calcLogLike() (Tree method) calcRates() (Gdasrv method) calculateBitKeyForInternalNodeFromChildren() (QuartetJoining method) calcUnconstrainedLogLikelihood1() (Data method) calcUnconstrainedLogLikelihood2() (Data method) changeDataTypeTo() (Alignment method) charsets() (in module p4.func) checkBigTInternalNodes() (QuartetJoining method) checkBitKeys() (QuartetJoining method) checkDupedTaxonNames() (Tree method) checkForAllGapColumns() (Alignment method) checkForBlankSequences() (Alignment method) checkForDuplicateSequences() (Alignment method) checkLengthsAndTypes() (Alignment method) checkNamesForDupes() (SequenceList method) checkPoint() (Mcmc method) (STMcmc method) checkSplitKeys() (Tree method) checkTaxNames() (Tree method) (Trees method) checkThatAllSelfNodesAreInTheTree() (Tree method) checkTranslation() (Alignment method) (Sequence method) chiSquaredProb() (in module p4.func)

clustalo() (SequenceList method) collapseClade() (Tree method) collapseNode() (Tree method) collapseNodesAndAddUnusedTaxa() (QuartetJoining method) combineWith() (TreePartitions method) Comp (class in p4.tree) compareSplits() (McmcCheckPointReader method) (TreePartitions method) compareSplitsAll() (McmcCheckPointReader method) compareSplitsBetweenTreePartitions() (in module p4.func) compoChiSquaredTest() (Data method) composition() (Alignment method) compositionEuclideanDistanceMatrix() (Alignment method) compoSummary() (Data method) compoTestUsingSimulations() (Tree method) compStatFromCharFreqs() (Tree method) concatenate() (Alignment method) consel() (Trees method) consensus() (TreePartitions method) constantMask() (Alignment method) constantSitesCount() (Alignment method) constantSitesProportion() (Alignment method) Constraints (class in p4.constraints) copyToTree() (Tree method) covarionStats() (Alignment method)

D

Data (class in p4.data) data (Tree property) dataType (Alignment attribute) decorateTreeWithBitKeys() (QuartetJoining method) deleteCStuff() (Tree method) detachRooter() (Tree method) dim (Alignment attribute) dirichlet1() (in module p4.func) dirichlet2() (in module p4.func) DistanceMatrix (class in p4.distancematrix) doSplash (Var attribute) draw() (Tree method) drawTopologyCompare() (Tree method) dump() (Alignment method) (Constraints method) (Data method) (in module p4.func) (McmcCheckPointReader method) (Model method) (NexusSets method) (Numbers method) (QuartetJoining method) (Sequence method) (SequenceList method) (Tree method) (TreePartitions method) (Trees method)

dupe() (Alignment method) (Data method) (Sequence method) (Tree method) dupeCharSet() (NexusSets method) dupeSubTree() (Tree method)

E

effectiveSampleSize() (in module p4.func) entropyMeanAndVariance() (Alignment method) entropyOfSites() (Alignment method) eps() (Tree method)

equates (Alignment attribute) examplesDir (Var property) excepthookEditor (Var property) excludeCharSet() (Alignment method)

F

factorial() (in module p4.func) fastme() (DistanceMatrix method) fileNames (Var attribute)

finishSplits() (TreePartitions method) fixCharsForLatex() (in module p4.func) flatTriangle() (DistanceMatrix method) fName (SequenceList attribute)

G

GAMMA_SHAPE_MAX (Var property) GAMMA_SHAPE_MIN (Var property) gappedMask() (Alignment method) Gdasrv (class in p4.tree) GeneticCode (class in p4.geneticcode) getAllGapsMask() (Alignment method) getAllLeafNames() (Tree method) getAnInputTreeForTheStartingTree() (QuartetJoining method) getBigQ() (Model method) getCharDiversityDistribution() (Alignment method) getCharDiversityOverSites() (Alignment method) getChildrenNums() (Tree method) getDegree() (Tree method) getEnoughCharsMask() (Alignment method) getEuclideanDistanceFromSelfDataToExpectedComposition() (Tree method) getKNodes() (QuartetJoining method) getKosiolAISGroups() (Alignment method) getLen() (Tree method) getLikelihoodTopologyInformativeSitesMask() (Alignment method) getMaskForAutapomorphies() (Alignment method) getMaskForCharDiversity() (Alignment method) getMinmaxChiSqGroups() (Alignment method) getNChildren() (Node method) getNodeNumsAbove() (Tree method) getNodeOnReferenceTreeCorrespondingToSelfRoot() (Tree method) getNodesOnReferenceTreeCorrespondingToSelfRoots() (Trees method)

getPreAndPostOrderAbove() (Tree method) getPreAndPostOrderAboveRoot() (Tree method) getProportionRange() (TreePartitions method) getProteinEmpiricalModelComp() (in module p4.func) getProteinEmpiricalModelRMatrix() (in module p4.func) getQuartetForFourTaxaInTrees() (QuartetJoining method) getQuartetsForXForNode() (QuartetJoining method) getSample() (PosteriorSamples method) getSeqNumsAbove() (Tree method) getSimpleBigF() (Alignment method) getSiteLikes() (Tree method) getSplitForTaxNames() (TreePartitions method) getSplitKeyFromTaxNames() (in module p4.func) getSplitsFromTree() (TreePartitions method) getSplitStringFromKey() (in module p4.func) getStartingTreeFromQuartet() (QuartetJoining method) getStartingTreeFromQuartet_highFrequencyFirst() (QuartetJoining method) getStartingTreeFromQuartet_randomTaxa() (QuartetJoining method) getTaxBitsString() (QuartetJoining method) getTree() (TreeFileLite method) getTreesWithSplit() (Trees method) getWeightCommandComment() (Tree method) gsl_meanVariance() (in module p4.func) (Numbers method) gsl_ran_dirichlet() (in module p4.func) gsl_ran_gamma() (in module p4.func)

H

harmonicMeanOfLogs() (Numbers method)

hasGapsOrAmbiguities() (Alignment method) histo() (Numbers method)

I

initDataParts() (Alignment method) inputTreesToSuperTreeDistances() (Tree method) (Trees method) interactiveHelper (Var property) isAncestorOf() (Node method) isBiRoot() (Tree method) isCompatibleWith() (Tree method) isDnaRnaOrProtein() (in module p4.func) isFullyBifurcating() (Tree method) isTriRoot() (Tree method) iterChildren() (Node method) iterDown() (Node method) iterInternals() (Node method) (Tree method)

iterInternalsNoRoot() (Tree method) iterInternalsNoRootPostOrder() (Tree method) iterInternalsNoRootPreOrder() (Tree method) iterInternalsPostOrder() (Tree method) iterLeaves() (Node method) iterLeavesNoRoot() (Tree method) iterLeavesPostOrder() (Tree method) iterLeavesPreOrder() (Tree method) iterNodes() (Tree method) iterNodesNoRoot() (Tree method) iterPostOrder() (Node method) (Tree method) iterPreOrder() (Node method) (Tree method)

K

KAPPA_MAX (Var property)

KAPPA_MIN (Var property)

L

ladderize() (Tree method) leftSibling() (Node method) lineUpLeaves() (Tree method)

listOfSplits() (Reduced method) locateAndCountLeavesInXSubTreeFromQuartet() (QuartetJoining method) lpml() (Mcmc method) ls() (in module p4.func)

M

majorityRuleConsensus() (Reduced method) makeSequenceForNameDict() (SequenceList method) makeSplitKeys() (Tree method) makeSplits_Off() (TreePartitions method) makeStartingQuartetFromAllTrees() (QuartetJoining method) makeTreeFromPartitions() (TreePartitions method) maskFromNexusCharacterList() (in module p4.func) matchedPairsTests() (Alignment method) matrixLowerTriangleToUpperTriangle() (in module p4.func) Mcmc (class in p4.mcmc) McmcCheckPointReader (class in p4.mcmccheckpointreader) mean() (in module p4.func) (Numbers method) meanNCharsPerSite() (Alignment method) (Data method) Model (class in p4.model) model (Tree property) modelFitTests() (Tree method) modelSanityCheck() (Tree method) modelSymbols (Var attribute) module p4.alignment p4.constraints p4.data p4.distancematrix p4.func p4.geneticcode p4.mcmc p4.mcmccheckpointreader p4.model p4.mrp p4.nexussets p4.node p4.pnumbers p4.posteriorsamples p4.quartetjoining p4.reducedstrictconsensus p4.sequence p4.sequencelist p4.stmcmc p4.supertreesupport p4.tree p4.treefilelite p4.treepartitions p4.trees p4.var

mrp() (in module p4.mrp) mrpSlice() (Alignment method) muscle() (SequenceList method)

N

nChar (Alignment property) (Sequence property) nChooseK() (in module p4.func) nEquates (Alignment property) newCharSet() (NexusSets method) newComp() (Tree method) newEmptyAlignment() (in module p4.func) newGdasrv() (Tree method) newick_allowSpacesInNames (Var attribute) newRMatrix() (Tree method) newtAndBrentPowellOptPassLimit (Var property) newtonRaftery94_eqn16() (in module p4.func) nextNode() (Tree method) nexus_allowAllDigitNames (Var attribute) nexus_allowUTREE (Var attribute) nexus_getAllCommandComments (Var property) nexus_getLineEndingsAsTokens (Var property) nexus_getP4CommandComments (Var property) nexus_getWeightCommandComments (Var property) nexus_ignoreFormatCommandSymbols (Var attribute) nexus_readBeastTreeCommandComments (Var attribute) nexus_warnSkipUnknownBlock (Var attribute) nexus_warnSwitchGapChar (Var attribute) nexus_warnSwitchMissingChar (Var attribute)

nexus_writeVisibleComments (Var property) nexusCheckName() (in module p4.func) nexusFixNameIfQuotesAreNeeded() (in module p4.func) nexusSets (Alignment attribute) NexusSets (class in p4.nexussets) nexusSets (Var attribute) nexusUnquoteAndDeUnderscoreName() (in module p4.func) nexusUnquoteName() (in module p4.func) nInternalNodes (Tree property) njUsingPaup() (DistanceMatrix method) nni() (Tree method) nni2() (Tree method) Node (class in p4.node) node() (Tree method) noGapsOrAmbiguitiesCopy() (Alignment method) nRootedTrees() (in module p4.func) nRootedTreesWithMultifurcations() (in module p4.func) nTax (Alignment property) (QuartetJoining property) (Tree property) (Trees property) nTrees (QuartetJoining property) Numbers (class in p4.pnumbers) nUnrootedTrees() (in module p4.func) nUnrootedTreesWithMultifurcations() (in module p4.func)

O

optLogLike() (Tree method)

optTest() (Tree method) orMasks() (Alignment method)

P

p4.alignment module p4.constraints module p4.data module p4.distancematrix module p4.func module p4.geneticcode module p4.mcmc module p4.mcmccheckpointreader module p4.model module p4.mrp module p4.nexussets module p4.node module p4.pnumbers module p4.posteriorsamples module p4.quartetjoining module p4.reducedstrictconsensus module p4.sequence module p4.sequencelist module

p4.stmcmc module p4.supertreesupport module p4.tree module p4.treefilelite module p4.treepartitions module p4.trees module p4.var module parseNewick() (Tree method) parseNexus() (Tree method) parts (Alignment attribute) patristicDistanceMatrix() (Tree method) pause() (QuartetJoining method) pDistances() (Alignment method) phylipDataMaxNameLength (Var attribute) PInvar (class in p4.tree) PINVAR_MAX (Var property) PINVAR_MIN (Var property) PIVEC_MAX (Var property) PIVEC_MIN (Var property) plot() (Numbers method) polar2square() (in module p4.func) popcount() (QuartetJoining method) (SuperTreeSupport method) popcountLimit() (SuperTreeSupport method) PosteriorSamples (class in p4.posteriorsamples) printReducedOutput() (SuperTreeSupport method) printSplitList() (SuperTreeSupport method) pruneSubTreeWithoutParent() (Tree method) pruneSubTreeWithParent() (Tree method) putGaps() (Alignment method)

Q

QuartetJoining (class in p4.quartetjoining)

quartetJoining() (QuartetJoining method)

R

randomizeTopology() (Tree method) randomSpr() (Tree method) randomTree() (in module p4.func) RATE_MAX (Var property) RATE_MIN (Var property) read() (in module p4.func) (McmcCheckPointReader method) (Numbers method) (TreePartitions method) readAndPop() (in module p4.func) readBipartitionsFromPaupLogFile() (Tree method) readFile() (in module p4.func) readJplace() (in module p4.func) readOpenPhylipFile() (Alignment method) readPhylipFile() (DistanceMatrix method) readPhyloXmlFile() (Tree method) recalculateSplitKeysOfNodeFromChildren() (Tree method) recipes() (in module p4.func) recodeDayhoff() (Alignment method) recodeProteinIntoGroups() (Alignment method) recodeRY() (Alignment method) reconnectSubTreeWithoutParent() (Tree method) reconnectSubTreeWithParent() (Tree method) Reduced (class in p4.reducedstrictconsensus) reducedConsensusProfile() (Reduced method) reducedMemQuick() (Reduced method) reducedQuick() (Reduced method) reducedStrictConsensus() (Reduced method)

refineKSubTree() (QuartetJoining method) RELRATE_MAX (Var property) RELRATE_MIN (Var property) removeAboveNode() (Tree method) removeEverythingExceptCladeAtNode() (Tree method) removeNode() (Tree method) removeRoot() (Tree method) renameForPhylip() (SequenceList method) (Tree method) reRoot() (Tree method) reseedCRandomizer() (in module p4.func) resetPartsContentFromSequences() (Alignment method) resetSequencesFromParts() (Alignment method) (Data method) resolve() (Tree method) resolvePolytomyAtNode() (Tree method) restoreDupeTaxa() (Tree method) restoreNamesFromRenameForPhylip() (SequenceList method) (Tree method) reverseComplement() (Sequence method) reverseMrp() (in module p4.mrp) rightmostChild() (Node method) RMatrix (class in p4.tree) rMatrixNormalizeTo1 (Var property) rMatrixProteinSpecs (Var attribute) rotateAround() (Tree method) run() (Mcmc method) (STMcmc method)

S

saveIndexTree() (SuperTreeSupport method) Sequence (class in p4.sequence) sequenceForNameDict (SequenceList attribute) SequenceList (class in p4.sequencelist) sequenceLists (Var attribute) sequences (SequenceList attribute) sequenceSlice() (Alignment method) setCharPartition() (Alignment method) setCStuff() (Tree method) setDim() (DistanceMatrix method) setEmpiricalComps() (Tree method) setGBlocksCharSet() (Alignment method) setModelComponentOnNode() (Tree method) setModelComponentsNNodes() (Tree method) setModelComponentsOnNodesRandomly() (Tree method) setModelThingsRandomly() (Tree method) setNewModel() (Tree method) setNexusSets() (Alignment method) (Tree method) setNGammaCat() (Tree method) setPInvar() (Tree method) setPreAndPostOrder() (Tree method) setRelRate() (Tree method) setTaxNames() (Trees method) setTerminalColor() (in module p4.func) setTerminalColour() (in module p4.func) setTextDrawSymbol() (Tree method) setTreeTaxBits() (QuartetJoining method) simpleBigXSquared() (Data method)

simpleCharCounts() (Alignment method) simpleConstantMask() (Alignment method) simpleConstantSitesCount() (Data method) simsForModelFitTests() (Tree method) simulate() (Tree method) sortListOfListsOnListElementNumber() (in module p4.func) sortListOfObjectsOn2Attributes() (in module p4.func) sortListOfObjectsOnAttribute() (in module p4.func) spaceDelimitedToTabDelimited() (in module p4.func) spaQ (STMcmc property) splash() (in module p4.func) splash2() (in module p4.func) spr() (Tree method) square2polar() (in module p4.func) STMcmc (class in p4.stmcmc) stringZapWhitespaceAndDigits() (in module p4.func) stripBrLens() (Tree method) studentsTStat() (in module p4.func) studentsTTest1() (in module p4.func) subsetUsingCharSet() (Alignment method) subsetUsingMask() (Alignment method) subTreeIsFullyBifurcating() (Tree method) summarizeMcmcPrams() (in module p4.func) summarizeModelComponentsNNodes() (Tree method) summarizeUnusedTaxa() (QuartetJoining method) SuperTreeSupport (class in p4.supertreesupport) superTreeSupport() (SuperTreeSupport method) symbols (Alignment attribute) symtestAsInIQTreeNaserKhdour() (Alignment method)

T

tailAreaProbability() (in module p4.func) (Numbers method) taxNames (Alignment property) (Tree property) taxSetIsASplit() (Tree method) testOverallFromAbabnehEtAl2006() (Alignment method) textDrawList() (Tree method) topologyDistance() (Tree method) topologyDistanceMatrix() (Trees method) topologyDistanceMetrics (Var attribute) tPickle() (Tree method) trackSplitsFromTree() (Trees method)

translate() (Alignment method) (GeneticCode method) (Sequence method) Tree (class in p4.tree) TreeFileLite (class in p4.treefilelite) TreePartitions (class in p4.treepartitions) treeProbabilities() (Trees method) Trees (class in p4.trees) trees (Var attribute) tryToAddAnyX() (QuartetJoining method) tryToAddAParticularX() (QuartetJoining method) tv() (Tree method) tvTopologyCompare() (Tree method)

U

uninstall() (in module p4.func) uniqueFile() (in module p4.func) unPickleMcmc() (in module p4.func)

unPickleSTMcmc() (in module p4.func) unsetTerminalColor() (in module p4.func) unsetTerminalColour() (in module p4.func)

V

val (Comp property) (Gdasrv property) Var (class in p4.var) variance() (in module p4.func)

verboseRead (Var attribute) verifyIdentityWith() (Tree method) versionAsDate() (in module p4.func) versionAsGitHash() (in module p4.func)

W

warnReadNoFile (Var attribute) which() (in module p4.func) which2() (in module p4.func) wipe() (Node method) wise2Table() (GeneticCode method) write() (NexusSets method) (Sequence method) (Tree method) writeExtended() (Reduced method) writeFasta() (Sequence method) (SequenceList method) writeFastaToBytesFlob() (SequenceList method) writeFastaToOpenFile() (Sequence method) writeFastaUppercase (Var attribute) writeInColor() (in module p4.func) writeInColour() (in module p4.func) writeIntersections() (Reduced method) writeMolphy() (Alignment method) writeNewick() (Tree method) (Trees method) writeNexus() (Alignment method) (Data method) (DistanceMatrix method) (NexusSets method) (Tree method) (Trees method)

writeNexusToOpenFile() (DistanceMatrix method) (NexusSets method) writePhylip() (Alignment method) (DistanceMatrix method) (Tree method) writePhylipToOpenFile() (DistanceMatrix method) writeProposalAcceptances() (Mcmc method) (McmcCheckPointReader method) (STMcmc method) writeProposalProbs() (Mcmc method) (McmcCheckPointReader method) (STMcmc method) writeSplits() (TreePartitions method) writeSwapMatrices() (McmcCheckPointReader method) writeSwapMatrix() (Mcmc method) (STMcmc method) writeSwapVector() (Mcmc method) writeSwapVectors() (McmcCheckPointReader method)

X

xSquared() (in module p4.func)